What you're referring to as "per diem" is really referred to as the Meals and Incidentals allowance and DOES NOT cover hotel expenses. It's only meals and incidentals. Incidentals includes little things like soap, laundry, etc. If you wanted to keep a separate tab for incidentals you can do that, you just take the incidentals portion out of your M&I allowance...I believe it's $3/day, but I'd double-check. If you wanted to do that, you'd take $49/day plus actual costs for incidentals. Keep those hotel receipts, usually good for a few thousand a year for us.
Ahhh, forgot you were an LLC, but an LLC is still a pass-through entity, so it really doesn't matter whether you actually pay yourself a wage or not. Again, if you're showing a loss on the year it's irrelevant.